[BioC] AFFX-BioB-3_at annotation

[Wu, Xiwei]

Ting-Yuan, 

Thank you for your prompt reply. Here is the code and session
information:

> library(hgu133plus2)
> get("AFFX-BioB-3_at", hgu133plus2ACCNUM)
[1] "AFFX-BIOB-3"
> get("AFFX-BioB-3_at", hgu133plus2UNIGENE)
[1] "Rn.103750"
> get("AFFX-BioB-3_at", hgu133plus2SYMBOL)
[1] "Fos"
> library(mouse4302)
> get("AFFX-BioB-3_at", mouse4302ACCNUM)
[1] "AFFX-BIOB-3"
> get("AFFX-BioB-3_at", mouse4302UNIGENE)
[1] "Rn.103750"
> get("AFFX-BioB-3_at", mouse4302SYMBOL)
[1] "Fos"
> library(mouse430a2)
> get("AFFX-BioB-3_at", mouse430a2ACCNUM)
[1] "AFFX-BIOB-3"
> get("AFFX-BioB-3_at", mouse430a2UNIGENE)
[1] "Rn.103750"
> get("AFFX-BioB-3_at", mouse430a2SYMBOL)
[1] "Fos"
> sessionInfo()
R version 2.2.0, 2005-10-07, i386-pc-mingw32 

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"
"datasets"  "base"     

other attached packages:
 mouse430a2   mouse4302 hgu133plus2 
   "1.10.0"    "1.10.0"    "1.10.0" 


Apparently, I am using the stable release BIOC1.7 annotation packages.
It seems that the problem is fixed in the developmental packages. Why
this probeset is not found in the developmental mouse430a2? It should be
there on the chip.

Xiwei

-----Original Message-----
From: Ting-Yuan Liu [mailto:tliu at fhcrc.org] 
Sent: Tuesday, April 04, 2006 6:11 PM
To: Wu, Xiwei
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] AFFX-BioB-3_at annotation


Hi Xiwei,

Could you give us more detail about this?  I cannot reproduce your
result:

> library(hgu133plus2)
> get("AFFX-BioB-3_at", hgu133plus2ACCNUM)
[1] "AFFX-BIOB-3"
> get("AFFX-BioB-3_at", hgu133plus2UNIGENE)
[1] NA
> library(mouse4302)
> get("AFFX-BioB-3_at", mouse4302UNIGENE)
[1] NA
> get("AFFX-BioB-3_at", mouse4302ACCNUM)
[1] "AFFX-BIOB-3"
> library(mouse430a2)
> get("AFFX-BioB-3_at", mouse430a2ACCNUM)
Error in get(x, envir, mode, inherits) : variable "AFFX-BioB-3_at" was
not found
> sessionInfo()
Version 2.3.0 Under development (unstable) (2006-01-04 r36984)
x86_64-unknown-linux-gnu 

attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics"  
"grDevices"
[7] "utils"     "datasets"  "base"     

other attached packages:
 mouse430a2   mouse4302 hgu133plus2  AnnBuilder     RSQLite         DBI 
  "1.11.23"   "1.11.23"   "1.11.23"    "1.9.16"     "0.4-0"     "0.1-9" 

It seems that our developmental annotation packages don't have such
mistakes.  Therefore, could you give us
(1) the code you generate this mistake, and
(2) the output of sessionInfo()
so that we could have more information about your system?

Thanks,
Ting-Yuan
______________________________________
Ting-Yuan Liu
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
______________________________________

On Tue, 4 Apr 2006, Wu, Xiwei wrote:

> Dear list,
>  
> It seems to me that no one has asked this question. In all of the 
> annotation packages I looked at, including HGU133plus2, mouse4302, 
> mouse430a2, AFFX-BioB-3_at are all annotated as FOS with a rat Unigene

> ID - Rn.103750. I thought it should be E coli bioB gene biotin 
> synthetase. Am I missing sth here?
> 
> Xiwei Wu, MD, PhD
> Director, Affymetrix Core Facility
> Research Scientist
> Department of Biomedical Informatics
> Beckman Research Institute
> City of Hope National Medical Center
> Duarte, CA 91010
> Phone: (626) 359-8111 ext. 65071
> 
> 
> "EMF <COH.ORG>" made the following annotations.
> ----------------------------------------------------------------------
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